caffMatch is a novel scaffolding tool based on Maximum-Weight Matching able to produce high-quality scaffolds from NGS data (reads and contigs). The tool is written in Python 2.7. It also includes a bash script wrapper that calls aligner in case one needs to first map reads to contigs (instead of providing .sam files).
The arguments accepted by ScaffMatch are:
-w) Working directory -- this is the directory where ScaffMatch files are stored. These are .sam files produced after mapping reads to contigs and the resulting scaffolds file `scaffolds.fa` fasta file;
-c) Contig fasta file;
-m) Command line argument with no options. It is used when .sam files are used instead of reads .fastq files. Do not use this option if you provide reads files;
-1) (Comma separated list of) either .fastq or .sam file(s) corresponding to the first read of the read pair;
-2) (Comma separated list of) either .fastq or .sam file(s) corresponding to the second read of the read pair;
-i) (Comma separated list of) insert size(s) of the library(-ies);
-s) (Comma separated list of) library(-ies) standard deviation(s) of insert size(s);
-t) Bundle threshold. Pairs of contigs supported by number of read pairs less than the value of this argument are discarded. Optional argument, by default it is equal to 5;
-g) Matching heuristics: use `max_weight` for Maximum Weight Matching heuristics with the Insertion step, use `backbone` for Maximum Weight Matching heuristics without the Insertion step, use `greedy` for Greedy Matching heuristics;
-l) Log file - where to store the logs. Optional argument. By default, stdout is used.
